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Indiana Jones' luck has finally run out. In 1941, he's stuck in a jail in Puerto Bolivar, Ecuador. When the U.S. Army comes knocking with a official release, Indy knows they'll want something big from him in exchange — like cracking the mystery of the fabled Hall of Records — a treasure trove that, legend says, allows you to read the future

On this adventure, Indy will not only have to outsmart and outmaneuver his enemies, he'll also have to figure out who his enemies are — because spies and traitors are gunning for him at every turn!

Indiana Jones works at an archaeological dig in Peru when a porter hands him a wanted poster of himself, accusing Jones of being a tomb robber. Suddenly, a burst of gunfire from the Peruvian army forces attacks Jones, who flees into the forests. Jones' attackers pursue him until he loses them using a false path. Jones swings over a chasm using a rope he had prepared beforehand in case he needed an escape. However, three men from the forces find Jones' chasm and see the rope still swinging slightly and retreat back.

Jones sneaks across the Peru-Ecuador border and plans to escape through the port city Puerto Bolivar. However, as Jones prepares to leave on a boat, three soldiers from the Peruvian army arrest Jones, handcuff him, and take him prisoner. Jones feigns tiredness as two soldiers enter his prison cell and tell him to move. Jones catches the two soldiers by surprise by swiftly knocking both of them out, but not before the second soldier calls for help. Two guards enter the cell as Jones takes a box of matches and a key ring from the second soldier's pocket.

Jones fires the fallen soldier's machine gun at the guards, who duck out of the line of fire. Jones uses the gun as a club to knock out the guards. To avoid attracting attention, Jones tries to act calmly as he walks down the streets. Jones uses the stolen matches to set fire to a shanty and distract the soldiers as he steals the truck, although he finds it does not have the keys in the ignition. Still with his hands handcuffed, Jones steers the truck down the ramp and lets it coast to a warehouse.

Two men greet Jones at the warehouse. A man that Jones soon recognizes as Colonel Musgrove and the Peruvian General Delgado hold all of Jones' recently stolen possessions. Musgrove helps Jones remove his handcuffs and claims that he came to Peru to alert the authorities that the wanted posters were faked. As they escape the warehouse, Musgrove introduces Jones to Major Nichols, who accompanies Jones and Musgrove to a nearby airplane.

Musgrove admits he was responsible for the wanted posters, and says it was the only way to find Jones while keeping his presence in South America as discreet as possible. Musgrove says that the Peruvian army was instructed to shoot only get Jones' attention. Musgrove explains that he needs Jones to find a dangerous ancient relic that fell into the wrong hands. Musgrove tells Jones that his archaeological friend Reginald Brooksbank had originally contacted them about the dangerous relic. Musgrove says Nazis killed Brooksbank while he was searching for the Akashic Hall of Records in Bimini. Jones agrees to help Musgrove find the Hall of Records.

As they fly to Costa Rica, Musgrove says that Brooksbank was capable of predicting future events in the war using the Hall of Records. Brooksbank had claimed he found the Hall of Records from an underground cavern from a dream. However, the Hall suddenly disappeared from Bimini, leaving behind only a small ball which makes anybody who directly touches it see a big lava pool with a giant statue over it. Nichols shows the ball and its properties to Jones, who says he recognizes the statue from the remains of Atlantis. To further prove that the Hall is real, Musgrove and Nichols show Jones a video tape of Brooksbank predicting his own unavoidable death and other future events. Brooksbank urges them to go to the rocks known as the Three Sisters in Costa Rica to find out where the Hall will re-materialize.

The plane refuels in Panama, and Jones decides he needs a shower and Corporal McGuiness shows him a locker room. However, after Jones finishes showering, a sergeant attacks Jones with multiple concealed weapons. As the two fight, Nichols and Guiness show up and Nichols shoots the man before Jones has a chance to interrogate him. Fifteen minutes later, Nichols tells McGuiness that Jones is dead. The news that Jones had died of "internal bleeding" travels fast.

Musgrove prepares another flight, this time with a replacement crew. It is revealed that Jones has faked his own death so they can get away. Jones drives Musgrove and Nichols to Santa Clara, leaving the plane as a red herring. Jones goes to the cantina belonging to his acquaintance el Martillo, the Hammer. Jones makes Musgrove buy everybody in the cantina drinks so that he can go in while everybody is happy. Jones tells Nichols that he does not trust Musgrove and goes in and tells Musgrove that he does not trust Nichols. Jones sneaks on the Hammer's blue pickup truck, leaving Nichols and Musgrove alone.

The driver tells Jones to look for a ride from the pilot Bert. Jones asks two men if they knew any pilots named Bert. The two drunken men jump Jones, and he shields himself using a Mayan figurine and knocks them out. A woman pilot introduces herself as Bert Brodowski and identifies the men as Tomás and Geraldo. Bert flies Jones to Palmar Sur in Costa Rica.

Back in Panama, Nichols and Musgrove head back to army air force base and tell everyone to be on the lookout for the man they had all previously thought dead. They find the pickup driver that Jones had identified as el Martillo and find that Jones is traveling to Costa Rica in Bert's biplane. Suddenly, Nichols turns on Musgrove and shoots him. Nichols notifies the Military Police that Musgrove has been shot, saying that someone shot him from outside. An MP says Nichols is still breathing and brings him to the infirmary.

Guided by Enrique, Jones finds the Three Sisters. Jones uses the marble-sized ball to discover where the Hall of Records is. Jones tells Bert that he needs to get to Uxmal, Mexico, using the ball to convince her. Led by Nichols, United States forces swarm the area and surround Bert's plane. Jones calls out Nichols as the mole in the group and Nichols orders Jones' arrest. Jones and Bert run through an inn and into some dense foliage that actually covers a ledge to a river.

After swimming down the river, Jones and Bert hatch a plan to get to Uxmal. Jones disguises himself as a pilot and argue with Bert as if he were her jealous boyfriend. Jones stands by the mail carrier biplane while Bert tells the soldiers guarding her plane that Major Nichols has forgiven her. However, the real mail carrier pilot shows up to meet his impostor and they start fighting. Bert swings by and Jones jumps onto the plane, but discovers that he has lost the box containing the ball from the Hall of Records. Nichols recovers the ball and finds the Three Sisters.

After refueling in Honduras and resting in Belize, Bert and Jones land near the Pyramid of the Sorcerer in Mexico. Jones tells Bert to leave him there and fly to Mérida in case Nichols shows up. Jones uses the four Mayan figurines to open the pyramid. Inside, he finds more ball objects that make him see into the past. The visions take him from the ancient times when a knight lost his sword to an incident when a young Jones had taken his father's sword off the wall.

Suddenly, an orb shows Jones a vision of Nichols standing outside the pyramid with an automatic pointed at Bert's head. Jones moves to leave, but stops when Reginald Brooksbank shows up. Brooksbank tells Jones that he had faked his death because Nichols had told him that Musgrove was a Nazi spy. Jones informs Brooksbank that the mole was actually Nichols. However, the mole himself shows up with an automatic braced against the side of Bert's head and her wrists tied. Jones says he saw the future of the battle, predicting Nichols' defeat and death in the jungle.

Jones moves to the side to avoid Nichols' ammo and cracks his whip at the weapon, causing Nichols to loosen both hands. Brooksbank gets hit by a bullet during the ensuing fight and Nichols runs into the Hall to avoid his fate, but the orbs explode when he touches too many at the same time. Two days after the incident, Musgrove recovers from his gunshot wound and talks with Jones at Mérida. Jones gives Brooksbank's predictions from the World Series to Bert.